Answer: There are several ways in which water might be getting inside your Hobie kayak hull
It is normal for a little bit of water to get inside the hull on any sit-on top kayak (there are various ways this can occur, explained below) and this is nothing to be worried about. However if there are large amounts of water getting into the hull further investigation and action is necessary.
Small amounts of water getting into hull: If you are noticing a cup or so of water inside the hull after a few hours on the water the chances are that it is coming in through the hatches, either the twist & stow or bow hatches. Well maintained twist & stow hatches do not leak water, though when water splashes up on deck some may end up resting in the small gap between the hatch and rim. As soon as you open that hatch it will probably leak down inside the hull - this is not a big deal. Hatches with poorly maintained gaskets (twisted, caked with sand and or gritty) will likely leak a bit of water even when closed.
Bow hatches don't usually seal quite as well as twist & stow hatches but this is rarely a problem because they generally sit well above the waterline and are all pretty much splash proof. Bow hatches with hatch liner buckets (that come as standard on Pro Anglers and optional for Revo & Quest 11, Revo & Quest 13 and Outback models) are more likely to leak as the hatch liner sits between the top of the hatch and seal underneath it. Although bow hatches on Adventure Island and Tandem Island models have seals on top and bottom, these are more likely to leak on rough days, especially if the bow is burying into the water. The first solution to this is to furl some of the sail so that the bow is not burying.
If the hatches aren't where water is getting in it may be that one or more of the various deck fittings aren't secured terribly well and have come a little loose. Inspect the fittings across the deck (mesh pockets, padeyes, eyelet posts, etc), re-screw any that feel a little loose and for best effect, use a little silicone where the component makes contact with the hull.
It can also pay to inspect the rudder line tubes that protrude from the stern (on all Miragedrive models, save for Pro Angler boats), especially if the rudder lines are somewhat close to the waterline level (such as Adventure Island and Outfitter for example). If the tubes don't appear to be perfectly seated into the holes, push them back into place. It's not a bad idea to use a little bit of silicon to help form a sure seal. It's also a great idea to use some Vaseline around the rudder lines where they protrude from the tubes. This will help minimize how much water can squeeze in through the rudder lines.
Large amounts of water getting into the hull: If you are seeing a lot of water getting inside the hull it could indicate a more serious issue that needs to be addressed - possibly a crack in the hull. The first thing to inspect is the drainage plug and make sure that a) it is indeed screwed in and that b) it's gasket and thread are in good order. If everything looks OK with the drainage plugs, inspect the following areas in the following order:
Scupper holes: It is possible for scupper holes to get damaged through in-correct insertion of a plug-in wheelcart, especially if the wheelcart itself is damaged and or has no end caps on the insertion posts. This is less likely to be the case on newer models with reinforced scupper holes, which Hobie introduced into most scupper holes in 2012. Check for cracks or holes in the scupper hole tubes. If you find damage you have likely found your problem. Contact your Hobie dealer for assistance with this.
Seat plugs: It is possible that a seat plug might be cracked (not Pro Angler models). This is less likely to be an issue on newer models (2013 and above) with Hobie's new Twist-Lock system, but more likely with older models. Inspect the holes where you plug your seat into and make sure there are no cracks or holes. If you find a problem, contact your Hobie dealer.
Seat well drainage scuppers: Inspect the drainage scuppers to make sure there are no cracks or holes. If you find a problem, contact your Hobie dealer.
Miragedrive well: Inspect the Miragedrive well to check for cracks or holes. It is rare for problems to occur here these days but was more common in earlier models. If you find a problem, contact your Hobie dealer.
If after inspecting these areas and everything looks OK, contact your local Hobie kayak dealer.